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The nation’s top military officer, in a deeply pessimistic assessment of the war in Afghanistan, said yesterday that due to years of neglect the United States is basically “starting over’’ in its battle against the radical Taliban movement and its Al Qaeda allies.

Acknowledging that public support for the war is waning, Navy Admiral Mike Mullen, the chairman of the Joint Chiefs of Staff, said that the US operation needs “12 to 18 months to turn this thing around.’’

“It is doable, but it is going to take some time,’’ he said, urging Americans to be patient.

With the intense focus until recently on fighting the war in Iraq - where the United States plans to keep nearly twice as many troops as in Afghanistan until at least early next year - he said that the Tali ban are far more potent than they were during the US invasion after the Sept. 11, 2001, terrorist attacks. The Taliban’s alliance with Osama bin Laden and other leaders of the Al Qaeda terrorist network, who he said are hiding in neighboring Pakistan’s lawless border region, is stronger than ever, he said.

“This is the eighth year, but there is a newness here,’’ Mullen told the Globe yesterday in Boston. “There is a starting again, or starting over. Iraq has been the focus, it hasn’t been Afghanistan.’’

Mullen’s wide-ranging interview came on a particularly bloody day in Afghanistan. Five car bombs simultaneously hit Kandahar, the country’s largest southern city, killing at least 41 people. And four more US troops were killed by another bomb in southern Afghanistan, bringing the August total to 41 and making this year already the deadliest yet of the war for American forces.

A Washington Post-ABC News poll this month found that 51 percent of Americans now say the war is not worth fighting and only 24 percent support sending more troops. President Obama, in a speech last week to the Veterans of Foreign Wars, conceded that the fighting has become more fierce but called Afghanistan “a war of necessity.’’

Military commanders on the ground told Richard Holbrooke, the president’s special envoy, during the weekend that the force was not big enough to defeat the Taliban, particularly in southern and eastern Afghanistan. The United States currently has about 68,000 troops dedicated to the war in Afghanistan, including 21,000 additional forces ordered by Obama earlier this year who are still flowing into the country.

Mullen, however, said he is awaiting a new assessment by the top commander in Afghanistan, Army General Stanley McChrystal, before making any recommendations on whether more US troops are needed to take on an increasingly emboldened Taliban.

But Mullen indicated he believes that, at a minimum, more specialists will be needed to train the Afghan security forces. “We all believe there is going to be a need to accelerate the training of the Afghanistan security forces, army and police, and that is going to take additional trainers,’’ he said.

Mullen, who became the nation’s top military officer in October 2007, visited patients at the Veterans Affairs medical center in Jamaica Plain earlier yesterday and plans to speak today at a Harvard Medical School conference about traumatic brain injuries, which have become much more common among combat troops.

He has expressed deepening concern in recent days about the progress of the war in Afghanistan, calling the situation “serious and deteriorating.’’ Yet his comments to Globe reporters and editors suggested outright alarm that without the right combination of cooperation from the Afghan government and the Pakistani military and an even greater US commitment, the Taliban could seize control of Afghanistan again.

“It is much more capable and much more potent than it was back’’ in 2001, he said, when the radical Islamic movement was toppled by the United States and its allies for harboring Al Qaeda. “And it is much broader than it was back then, and much deeper.’’

He also said that the Taliban’s ties to Al Qaeda leaders have been strengthened as the United States has trained its attention on Iraq. “The Taliban is much closer to Al Qaeda than it used to be,’’ Mullen said. “They are much more affiliated with each other than they were a few years ago. Call it a federation.’’

He added that Al Qaeda is “still very focused on trying to advance this corrupt view of Islam as far as they can. And one of the ways they do that is to focus on eliminating and killing as many Americans and Westerners as they can.’’

The US military, however, is behind the curve and struggling to retake control of the situation, Mullen said.

For one, the focus on Iraq has meant that there are too few American troops with experience in Afghanistan, requiring precious time for new units to get up to speed upon arriving in the country.

“I’d like to take people who have been to Afghanistan and send them back to leverage the cultural awareness and language awareness, which are critical pieces,’’ Mullen said. “The problem is I don’t have that many because I haven’t had that many in Afghanistan.’’

But Mullen dismissed calls by some specialists that the United States should immediately seek to negotiate with some elements of the Taliban who may be willing to put down their arms in exchange for a political stake in the Afghan government. General David Petraeus, who is overseeing US forces in both Afghanistan and Iraq, in recent weeks has also suggested that negotiations with some members of the Taliban could help reduce violence in parts of Afghanistan.

“I am one that believes that we need to negotiate . . . from a position of strength,’’ Mullen said. “We are not in a position of strength.’’